Post-transcriptional control of gene expression: Effectors of mRNA decay

Molecular Microbiology

Volumn 49, Issue 1, 2003, Pages 267-276

  Arraiano, Cecília Maria ^a   Maquat, Lynne Elizabeth ^b  

^a INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^b UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; MESSENGER RNA; NUCLEASE; PROTEIN C FOS; RIBONUCLEASE; RIBOZYME;

COMPLEX FORMATION; CONFERENCE PAPER; GENE EXPRESSION REGULATION; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; RNA DEGRADATION; STOP CODON; TRANSCRIPTION REGULATION; TRANSLATION INITIATION;

ANIMALS; BACTERIAL PROTEINS; GENE EXPRESSION REGULATION; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; RIBONUCLEASES; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA STABILITY; RNA, CATALYTIC; RNA, MESSENGER;

EID: 0037708992     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2003.03545.x     Document Type: Conference Paper

References (64)

1. Baginsky, S., Shteiman-Kotler, A., Liveanu, V., Yehudai-Resheff, S., Bellaoui, M., Settlage, R.E., et al. (2001) Chloroplast PNPase exists as a homo-multimer enzyme complex that is distinct from the Escherichia coli degradosome. RNA 7: 1464-1475.
2. Beran, R.K., and Simons, R.W. (2001) Cold-temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation. Mol Microbiol 39: 112-125.
3. Bernstein, J.A., Khodursky, A.B., Lin, P.H., Lin-Chao, S., and Cohen, S.N. (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA 99: 9697-9702.
4. Butler, J.S. (2002) The yin and yang of the exosome. (2002). Trends Cell Biol 12: 90-96.
5. Cairrão, F., Chora, A., Zilhão, R., Carpousis, A.J., and Arraiano, C.M. (2001) RNase II levels change according to the growth conditions: characterization of gmr, a new Escherichia coli gene involved in the modulation of RNase II. Mol Microbiol 39: 1550-1561.
6. Carpousis, A.J., and Dreyfus, M. (2003) mRNA decay and RNA-degrading machines in prokaryotes and eukaryotes. In Protein Synthesis and Ribosome Structure. Nierhaus, K.H. (ed.) Wiley-VCH (in press).
7. Carpousis, A.J., Van Houwe, G., Ehretsmann, C., and Krisch, H.M. (1994) Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76: 889-900.
8. Chen, C.Y., Gherzi, R., Ong, S.E., Chan, E.L., Raijmakers, R., Pruijn, G.J., et al. (2001) AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107: 451-464.
9. Cheng, Z.F., Zuo, Y., Li, Z., Rudd, K.E., and Deutscher, M.P. (1998) The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J Biol Chem 273: 14077-14080.
10. Coburn, G.A., Miao, X., Briant, D.J., and Mackie, G.A. (1999) Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEAD-box RNA helicase. Genes Dev 13: 2594-2603.
11. Cohen, S.N., and McDowall, K.J. (1997) RNase E: still a wonderfully mysterious enzyme. Mol Microbiol 23: 1099-1106.
12. Dahlberg, J.E., Lund, E., and Goodwin, E.B. (2003) Nuclear translation: What's the evidence? RNA 9: 1-8.
13. Decker, C.J., and Parker, R. (2002) mRNA decay enzymes: Decappers conserved between yeast and mammals. Proc Natl Acad Sci USA 99: 12512-12514.
14. Diwa, A.A., Jiang, X., Schapira, M., and Belasco, J.G. (2002) Two distinct regions on the surface of an RNA-binding domain are crucial for RNase E function. Mol Microbiol 46: 959-969.
15. Donovan, W.P., and Kushner, S.R. (1986) Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc Natl Acad Sci USA 83: 120-124.
16. Dreyfus, M., and Régnier, P. (2002) The poly (A) tail of mRNAs: Bodyguard in eukaryotes, scavenger in bacteria. Cell 111: 611-613.
17. Feng, Y., Vickers, T.A., and Cohen, S.N. (2002) The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection. Proc Natl Acad Sci USA 99: 14746-14751.
18. Goodwin, E.B., and Ellis, R.E. (2002) Turning clustering loops: sex determination in Caenorhabditis elegans. Curr Biol 12: R111-R120.
19. Grosset, C., Chen, C.Y., Xu, N., Sonenberg, N., Jacquemin-Sablon, H., and Shyu, A.B. (2000) A mechanism for translationally coupled mRNA turnover: interaction between the poly (A) tail and a c-fos RNA coding determinant via a protein complex. Cell 103: 29-40.
20. Gudikote, J.P., and Wilkinson, M.F. (2002) T-cell receptor sequences that elicit strong down-regulation of premature termination codon-bearing transcripts. EMBO J 21: 125-134.
21. Iborra, F.J., and Cook, P.R. (2002) The interdependence of nuclear structure and function. Curr Opin Cell Biol 14: 780-785.
22. Iborra, F.J., Jackson, D.A., and Cook, P.R. (2001) Coupled transcription and translation within nuclei of mammalian cells. Science 293: 1139-1142.
23. Ishigaki, Y., Li, X., Serin, G., and Maquat, L.E. (2001) Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20. Cell 106: 607-617.
24. Kawasaki, H., and Taira, K. (2002a) Identification of genes by hybrid ribozymes that couple cleavage activity with the unwinding activity of an endogenous RNA helicase. EMBO Report 3: 443-450.
25. Kawasaki, H., and Taira, K. (2002b) A functional gene discovery in the Fas-mediated pathway to apoptosis by analysis of transiently expressed randomized hybrid-ribozyme libraries. Nucleic Acids Res 30: 3609-3614.
26. Lee, K., Bernstein, J.A., and Cohen, S.N. (2002) RNase G complementation of the rne null mutation identifies functional interrelationships with RNase E in Escherichia coli. Mol Microbiol 43: 1445-1456.
27. Lejeune, F., Ishigaki, Y., Li, X., and Maquat, L.E. (2002) The exon junction complex is detected on CBP80-bound but not elF4E-bound mRNA in mammalian cells: dynamics of mRNP remodeling. EMBO J 21: 3536-3545.
28. Leroy, A., Vanzo, N.F., Sousa, S., Dreyfus, M., and Carpousis, A.J. (2002) Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA. Mol Microbiol 45: 1231-1243.
29. Li, Z., Reimers, S., Pandit, S., and Deutscher, M.P. (2002) RNA quality control: degradation of defective transfer RNA. EMBO J 21: 1132-1138.
30. Lykke-Andersen, J. (2002) Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol 22: 8114-8121.
31. Mackie, G.A. (1998) Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395: 720-723.
32. Maquat, L.E. (2002) NASty effects on fibrillin pre-mRNA splicing: another case of ESE does it, but proposals for translation-dependent splice site choice live on. Genes Dev 16: 1743-1753.
33. Marujo, P.E., Hajnsdorf, E., Le Derout, J., Andrade, R., Arraiano, C.M., and Régnier, P. (2000) RNase II removes the oligo (A) tails that destabilize the rpsO mRNA of Escherichia coli. RNA 6: 1185-1193.
34. Marzluff, W.F., and Duronio, R.J. (2002) Histone mRNA expression: multiple levels of cell cycle regulation and important developmental consequences. Curr Opin Cell Biol 14: 692-699.
35. Mathy, N., Jarrige, A.C., Robert-Le Meur, M., and Portier, C. (2001) Increased expression of Escherichia coli polynucleotide phosphorylase at low temperatures is linked to a decrease in the efficiency of autocontrol. J Bacteriol 183: 3848-3854.
36. Mendell, J.T., Rhys, C.M., and Dietz, H.C. (2002) Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts. Science 298: 419-422.
37. Mitchell, P., and Tollervey, D. (2000) Musing on the structural organization of the exosome complex. Nat Struct Bio 10: 843-846.
38. Mohanty, B.K., and Kushner, S.R. (2000) Polynucleotide phosphorylase functions both as a 3′ right-arrow 5′ exonuclease and a poly (A) polymerase in Escherichia coli. Proc Natl Acad Sci USA 97: 11966-11971.
39. Mohanty, B.K., and Kushner, S.R. (2002) Polyadenylation of Escherichia coli transcripts plays an integral role in regulating intracellular levels of polynucleotide phosphorylase and RNase E. Mol Microbiol 45: 1315-1324.
40. Muhlrad, D., and Parker, R. (1994) Premature translational termination triggers mRNA decapping. Nature 370: 578-581.
41. Mukherjee, D., Gao, M., O'Connor, J.P., Raijmakers, R., Pruijn, G., Lutz, C.S., and Wilusz, J. (2002) The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements. EMBO J 21: 165-174.
42. Nakamura, Y., and Ito, K. (2002) A tripeptide discriminator for stop codon recognition. FEBS Lett 514: 30-33.
43. Nathanson, L., Xia, T., and Deutscher, M. (2003) Nuclear protein synthesis: a re-evaluation. RNA 9: 9-13.
44. Otero, L.J., Devaux, A., and Standart, N. (2001) A 250-nucleotide UA-rich element in the 3′ untranslated region of Xenopus laevis Vg1 mRNA represses translation both in vivo and in vitro. RNA 7: 1753-1767.
45. Ptushkina, M., Berthelot, K., vonder Haar, T., Geffers, L., Warwicker, J., and McCarthy, J.E. (2001) A second elF4E protein in Schizosaccharomyces pombe has distinct elF4G-binding properties. Nucleic Acids Res 29: 4561-4569.
46. Ramirez, C.V., Vilela, C., Berthelot, K., and McCarthy, J.E. (2002) Modulation of eukaryotic mRNA stability via the cap-binding translation complex elF4F. J Mol Biol 318: 951-962.
47. Régnier, P., and Arraiano, C.M. (2000) Degradation of mRNA in bacteria: emergence of ubiquitous features. Bioessays 22: 235-244.
48. Sachs, M.S., Wang, Z., Gaba, A., Fang, P., Belk, J., Ganesan, R., et al. (2002) Toeprint analysis of the positioning of translation apparatus components at initiation and termination codons of fungal mRNAs. Methods 26: 105-114.
49. Salehi, Z., Geffers, L., Vilela, C., Birkenhager, R., Ptushkina, M., Berthelot, K., et al. (2002) A nuclear protein in Schizosaccharomyces pombe with homology to the human tumour suppressor Fhit has decapping activity. Mol Microbiol 46: 49-62.
50. Senger, B., Lafontaine, D.L., Graindorge, J.S., Gadar, O., Camasses, A., Sanni, A., et al. (2001) The nucle (ol) ar Tif6p and Efl1p are required for a late cytoplasmic step of ribosome synthesis. Mol Cell 8: 1363-1373.
51. Si, K., and Maitra, U. (1999) The Saccharomyces cerevisiae homologue of mammalian translation initiation factor 6 does not function as a translation initiation factor. Mol Cell Biol 19: 1416-1426.
52. Stevens, A., Wang, Y., Bremer, K., Zhang, J., Hoepfner, R., Antoniou, M., et al. (2002) Beta-Globin mRNA decay in erythroid cells: UG site-preferred endonucleolytic cleavage that is augmented by a premature termination codon. Proc Natl Acad Sci USA 99: 12741-12746.
53. Storz, G. (2002) An expanding universe of noncoding RNAs. Science 296: 1260-1262.
54. Torchet, C., Bousquet-Antonelli, C., Milligan, L., Thompson, E., Kufel, J., and Tollervey, D. (2002) Processing of 3′-extended read-through transcripts by the exosome can generate functional mRNAs. Mol Cell 9: 1285-1296.
55. Van Dijk, E., Cougot, N., Meyer, S., Babajko, S., Wahle, E., and Seraphin, B. (2002) Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J 21: 6915-6924.
56. Vanzo, N.F., Li, Y.S., Py, B., Blum, E., Higgins, C.F., Raynal, L.C., Krisch, H.M., and Carpousis, A.J. (1998) Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev 12: 2770-2781.
57. Vasudevan, S., and Peltz, S.W. (2001) Regulated ARE-mediated mRNA decay in Saccharomyces cerevisiae. Mol Cell 7: 1191-1200.
58. Vilela, C., Velasco, C., Ptushkina, M., and McCarthy, J.E. (2000) The eukaryotic mRNA decapping protein Dcp1 interacts physically and functionally with the elF4F translation initiation complex. EMBO J 19: 4372-4382.
59. Wang, Z., and Kiledjian, M. (2001) Functional link between the mammalian exosome and mRNA decapping. Cell 107: 751-762.
60. Wang, Z., Jiao, X., Carr-Schmid, A., and Kiledjian, M. (2002a) The hDcp2 protein is a mammalian mRNA decapping enzyme. Proc Natl Acad Sci USA 99: 12663-12668.
61. Wang, J., Gudikote, J.P., Olivas, O.R., and Wilkinson, M.F. (2002b) Boundary-independent polar nonsense-mediated decay. EMBO Rep 3: 274-279.
62. Yehudai-Resheff, S., Hirsh, M., and Schuster, G. (2001) Polynucleotide phosphorylase functions as both an exonuclease and a poly (A) polymerase in spinach chloroplasts. Mol Cell Biol 21: 5408-5416.
63. Zangrossi, S., Briani, F., Ghisotti, D., Regonesi, M.E., Tortora, P., and Deho, G. (2000) Transcriptional and post-transcriptional control of polynucleotide phosphoryrase during cold acclimation in Escherichia coli. Mol Microbiol 36: 1470-1480.
64. Zuo, Y., and Deutscher, M.P. (2001) Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res 29: 1017-1026.